gentoo resync : 31.08.2021

6 files changed, 0 insertions, 160 deletions

diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
deleted file mode 100644
index ae2d7f82a568..000000000000
--- a/sci-biology/psipred/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX 3.1-Makefile.patch 1103 BLAKE2B ba9c5a7f60d62d66d1cd5a5e9b0a68ffe5c99124d02eae1924ffe92ecb2d24d7224e5bd0b37db3cf17da4f39d3c8b6b53e04466da8976e71910b9dcea9bc59ab SHA512 6e0daf4478b5b992ed1647bf653320b18cd2582ca69ebe761654bd4bd9c9c46b7de183ae84a28582cb5543603362eb7eb6c306ff562c3ec18c292d89480fd127
-AUX 3.1-path.patch 1128 BLAKE2B ea445427fe2ff574028b3d82ae353da5a1dfe3f5c7fade419287f6dc2e819471b4ec007dfee7cf71a1c958082a8dfa83acd5046208e0a7b16c07d90cdd68073f SHA512 e6201669db910f074bb13d1b781416d8d99300f328147cccd7755d5d6595b25aa45353f6da6566f225a067e94ab8ee41ea89bfd75cf2cdf2c076481707acf88c
-AUX 3.2-fgets.patch 427 BLAKE2B dba911ef9d28c230e38d326336fa7adfae31ffafd225d525968f58b1013df2f5812b0c678f37576714c7bfa396c7378b2e1201f8c6b2bea844c2e042eea7c0ec SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb
-DIST psipred3.5.tar.gz 1101579 BLAKE2B 2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2
-DIST tdbdata.tar.gz 40241247 BLAKE2B c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c
-EBUILD psipred-3.5.ebuild 1215 BLAKE2B b51ae7660ff58dd8d8c738b0019cf935afa8e4049af536065348a5afdf4ac8bba3e8d49fbd456de633a6ab471a3a4c4dee126e213c3b76a8ca75401dbbc0be2c SHA512 dc506a260d7cefb6b632dae25410860c9efc2561581735eabdbf321c635b4347f1a8ba911abb326c7bf80d85b3ae945b483d538e12f21ef3255c5b3edc8a4e17
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch
deleted file mode 100644
index 0c70b6868565..000000000000
--- a/sci-biology/psipred/files/3.1-Makefile.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index abed8af..26061fa 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -6,9 +6,9 @@
- #### CFLAGS	Flags to pass to C compiler.
- 
- INCDIR		= .
--CC		= cc
-+CC		?= gcc
- 
--CFLAGS		= -O
-+CFLAGS		?= -O2
- LIBS		= -lm
- 
- all:		psipred psipass2 chkparse seq2mtx pfilt
-@@ -20,16 +20,16 @@ clean:
- 		/bin/rm -f psipred psipass2 chkparse seq2mtx pfilt
- 
- psipred:	sspred_avpred.c ssdefs.h sspred_net.h
--		$(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred
-+		$(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred
- 
- psipass2:	sspred_hmulti.c ssdefs.h sspred_net2.h
--		$(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
-+		$(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
- 
- chkparse:	chkparse.c
--		$(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse
-+		$(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse
- 
- seq2mtx:	seq2mtx.c
--		$(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
-+		$(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
- 
- pfilt:		pfilt.c
--		$(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt
-+		$(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt
diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch
deleted file mode 100644
index 564e9c8a1ef9..000000000000
--- a/sci-biology/psipred/files/3.1-path.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/runpsipred b/runpsipred
-index 4ccf44e..34dee99 100755
---- a/runpsipred
-+++ b/runpsipred
-@@ -14,13 +14,13 @@
- set dbname = uniref90filt
- 
- # Where the NCBI programs have been installed
--set ncbidir = /usr/local/bin
-+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
- 
- # Where the PSIPRED V2 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
- 
- # Where the PSIPRED V2 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
- 
- set basename = $1:r
- set rootname = $basename:t
-diff --git a/runpsipred_single b/runpsipred_single
-index 1f7680b..7bd5bc3 100755
---- a/runpsipred_single
-+++ b/runpsipred_single
-@@ -10,10 +10,10 @@
- # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
- 
- # Where the PSIPRED V3 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
- 
- # Where the PSIPRED V3 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
- 
- set basename = $1:r
- set rootname = $basename:t
diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch
deleted file mode 100644
index ec06d141ee34..000000000000
--- a/sci-biology/psipred/files/3.2-fgets.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
-index 37b1332..4f04ab6 100644
---- a/src/sspred_avpred.c
-+++ b/src/sspred_avpred.c
-@@ -223,7 +223,7 @@ predict(int argc, char **argv)
- int             getmtx(FILE *lfil)
- {
-     int             aa, i, j, naa;
--    char            buf[256], *p;
-+    char            buf[65536], *p;
-     
-     if (fscanf(lfil, "%d", &naa) != 1)
- 	fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/psipred/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild
deleted file mode 100644
index f5619ef4b544..000000000000
--- a/sci-biology/psipred/psipred-3.5.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch prefix toolchain-funcs versionator
-
-#MY_P="${PN}$(delete_all_version_separators)"
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Protein Secondary Structure Prediction"
-HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
-SRC_URI="
-	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
-	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
-
-LICENSE="psipred"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	app-shells/tcsh
-	sci-biology/ncbi-tools
-	sci-biology/update-blastdb"
-DEPEND=""
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
-	rm -f bin/*
-	epatch \
-		"${FILESDIR}"/3.1-Makefile.patch \
-		"${FILESDIR}"/3.1-path.patch \
-		"${FILESDIR}"/3.2-fgets.patch
-	eprefixify runpsipred*
-	emake -C src clean
-}
-
-src_compile() {
-	emake -C src CC=$(tc-getCC)
-}
-
-src_install() {
-	emake -C src DESTDIR="${D}" install
-	dobin runpsipred* bin/* BLAST+/runpsipred*
-	insinto /usr/share/${PN}
-	doins -r data
-	dodoc README
-}
-
-pkg_postinst() {
-	elog "Please use the update_blastdb.pl in order to"
-	elog "maintain your own local blastdb"
-}